"This is just the progression of things that happen in an organization when new people take over," Fleita told ESPNChicago.com's Bruce Levine. "I've enjoyed my time with the Cubs. I think we've accomplished a lot of good things here."

The Cubs also fired manager of baseball information Chuck Wasserstrom, who had been a Cubs employee for over 25 years, having started out in the media relations department in 1986. President of baseball operations Theo Epstein said Wednesday that more front-office changes were imminent for the 45-70 Cubs.

Fleita joined the organization in 1995. He was the manager of the club's Class A affiliate and also oversaw extended spring training.

"All of us with the Cubs owe Oneri a debt of gratitude for his tremendous service to the organization over many years," Epstein said in a statement. "Oneri has impacted countless people here in a positive way, and we wish him well as he continues his career elsewhere."

After spending time as an area scout and coordinator of Latin America operations, Fleita was promoted to director of player development, where he helped groom current closer Carlos Marmol and shortstop Starlin Castro.

"I feel real bad," Castro said. "He was like my father. I talked to him all the time here and in the Dominican. I just feel real bad but it's a business."

Marmol said Fleita gave him the opportunity to switch from catcher to pitcher.

"I'm sad for him because I know Fleita and he knows me since I was 16," Marmol said. "This is the guy that gave me the opportunity in the minor leagues and it was hard for me to hear that. He did a lot of good things for me and I feel very sad.

"Oh yeah, no doubt [he was a father figure]. He knew me since I was 16 and I learned a lot from him. I feel very sad for him. He gave a lot of players opportunities, especially in the Dominican. He's great out there and everybody loves him there. That's what I see, everybody, players. He's a nice person, too."

Fleita was given a four-year extension last September before Epstein and general manager Jed Hoyer were hired. Fleita became expendable when Epstein brought in Jason McLeod as vice president of scouting and player development.

Epstein says Fleita is "free and clear" to pursue opportunities with other organizations.

Although other changes will be made, assistant general manager Randy Bush is expected to remain with the Cubs.

"Randy is in very good standing as assistant general manager," Epstein said. "He will continue in that role as a strong asset and has been a big help through the transition. This is an unfortunate part of the business. It is my responsibility to identify the structure that makes the most sense for the Cubs going forward and that comes with some difficult decisions."

Manager of statistical analysis Ari Kaplan has been reassigned as a consultant for chairman Tom Ricketts.

ESPNChicago.com's Doug Padilla contributed to this report. Information from The Associated Press was used in this report.